Variant report

Variant	rs6760379
Chromosome Location	chr2:55279536-55279537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr2:55271552-55280181	IMR90	lung:	n/a	chr2:55276840-55276850
2	FOS	chr2:55278214-55280128	MCF10A-Er-Src	breast:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55279171-55279183 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278506-55278517 chr2:55278401-55278411
3	CTCF	chr2:55279420-55279570	NHEK	skin:	n/a	n/a
4	CTCF	chr2:55279420-55279570	HA-sp	spinal cord:	n/a	n/a
5	RUNX3	chr2:55279196-55279646	GM12878	blood:	n/a	n/a
6	MAZ	chr2:55279132-55279636	GM12878	blood:	n/a	n/a
7	CUX1	chr2:55279152-55279746	K562	blood:	n/a	n/a
8	EP300	chr2:55279348-55279548	GM12878	blood:	n/a	n/a
9	CUX1	chr2:55279158-55279611	GM12878	blood:	n/a	n/a
10	CTCF	chr2:55279460-55279610	Caco-2	colon:	n/a	n/a
11	CTCF	chr2:55279400-55279550	HMF	breast:	n/a	n/a
12	CTCF	chr2:55274353-55279779	A549	lung:	n/a	n/a
13	POLR2A	chr2:55274556-55280140	IMR90	lung:	n/a	n/a
14	STAT3	chr2:55279004-55279820	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr2:55279480-55279556	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr2:55279234-55279554	GM12878	blood:	n/a	n/a
17	RUNX3	chr2:55279121-55279691	GM12878	blood:	n/a	n/a
18	EP300	chr2:55279248-55280041	K562	blood:	n/a	n/a
19	NFIC	chr2:55279204-55279660	GM12878	blood:	n/a	n/a
20	CTCF	chr2:55279307-55279602	K562	blood:	n/a	n/a
21	BHLHE40	chr2:55279252-55279542	GM12878	blood:	n/a	n/a
22	JUND	chr2:55279376-55279627	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55276798..55279791-chr2:55841794..55843892,2	K562	blood:
2	chr2:55278226..55280278-chr2:55389625..55391199,2	MCF-7	breast:
3	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
4	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
5	chr2:55278333..55279964-chr2:55343174..55345064,2	MCF-7	breast:
6	chr2:55278606..55281085-chr2:55289009..55290511,2	K562	blood:
7	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
8	chr2:55278300..55281080-chr2:55325086..55327233,3	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000162994	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000266376	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10173203	0.87[EUR][1000 genomes]
rs13387836	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3198123	0.82[EUR][1000 genomes]
rs7601895	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:55273400-55279800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:55274200-55279600	Active TSS	HMEC	breast
4	chr2:55275400-55279600	Active TSS	A549	lung
5	chr2:55275800-55280000	Active TSS	NHLF	lung
6	chr2:55277800-55279800	Active TSS	Right Atrium	heart
7	chr2:55278000-55279600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr2:55278000-55280000	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr2:55278000-55280000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:55278000-55280200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:55278200-55279800	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr2:55278200-55279800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr2:55278200-55280000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr2:55278200-55280000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr2:55278200-55282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55278200-55288800	Weak transcription	Lung	lung
17	chr2:55278400-55279800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:55278400-55280000	Flanking Active TSS	Dnd41	blood
19	chr2:55278400-55280200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:55278600-55279600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:55278600-55279800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:55278600-55279800	Flanking Active TSS	HUVEC	blood vessel
23	chr2:55278600-55279800	Flanking Active TSS	NH-A	brain
24	chr2:55278600-55280200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr2:55278600-55281000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:55278600-55281600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:55278600-55282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:55278800-55279600	Enhancers	Brain Anterior Caudate	brain
29	chr2:55278800-55279800	Enhancers	Brain Substantia Nigra	brain
30	chr2:55278800-55279800	Enhancers	Fetal Heart	heart
31	chr2:55278800-55279800	Active TSS	Fetal Thymus	thymus
32	chr2:55278800-55280600	Active TSS	K562	blood
33	chr2:55278800-55282200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:55278800-55283200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:55278800-55283200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:55279000-55279600	Enhancers	Adipose Nuclei	Adipose
39	chr2:55279000-55279600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:55279000-55279800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr2:55279000-55279800	Enhancers	Colon Smooth Muscle	Colon
42	chr2:55279000-55279800	Enhancers	Fetal Intestine Small	intestine
43	chr2:55279000-55279800	Enhancers	Fetal Stomach	stomach
44	chr2:55279000-55279800	Enhancers	Rectal Smooth Muscle	rectum
45	chr2:55279000-55279800	Enhancers	NHDF-Ad	bronchial
46	chr2:55279000-55280000	Enhancers	Duodenum Mucosa	Duodenum
47	chr2:55279000-55280000	Enhancers	Fetal Lung	lung
48	chr2:55279000-55280200	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr2:55279000-55280400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr2:55279000-55282000	Enhancers	Primary B cells from peripheral blood	blood

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